bootstrapParallel: Bootstrap biotic stations and acoustic data

Description Usage Arguments Value

View source: R/rstox_boostrap.r

Description

Resample (bootstrap) trawl stations based on survey (Cruise) number and station numbers (SerialNo) to estimate uncertainty in estimates.

Usage

1
2
3
4
5
bootstrapParallel(projectName, assignments, psuNASC = NULL,
  stratumNASC = NULL, resampledNASC = NULL, nboot = 5,
  startProcess = "TotalLengthDist", endProcess = "SuperIndAbundance",
  seed = 1, cores = 1, baseline = NULL, msg = TRUE,
  parameters = list(), sorted = TRUE)

Arguments

projectName

The name or full path of the project, a baseline object (as returned from getBaseline or runBaseline, og a project object (as returned from openProject).

assignments

Trawl assignment from baseline.

psuNASC

MeanNASC from baseline.

stratumNASC

Strata NASC estimates from getNASCDistr(baseline).

resampledNASC

Resampled NASC distribution.

nboot

Number of bootstrap replicates.

startProcess

The start process of the bootstrapping, being the first process before which biostations has been assigned and NASC values have been calculated.

endProcess

The end process of the bootstrapping, being the process returning a matrix containing the following columns: "Stratum", "Abundance", "weight", and grouping variables such as "age", "SpecCat", "sex".

seed

The seed for the random number generator (used for reproducibility).

cores

An integer giving the number of cores to run the bootstrapping over.

baseline

Optional: a StoX baseline object returned from runBaseline().

msg

Logical: if TRUE print messages from runBaseline().

parameters

Parameters set by user in Stox (only kept for compatibility with older versions);.

parameters$nboot

Number of bootstrap replicates

parameters$seed

The seed for the random number generator (used for reproducibility)

sorted

Should the data be sorted prior to sampling?

Value

list with (1) the abundance by length in the orginal model, (2) the abundance by length in the bootstrap run, (3) the abundance by super individuals in the orginal model, (4) the abundance by super individuals in the bootstrap run


Sea2Data/Rstox documentation built on April 18, 2018, 11:11 p.m.